Back to PLS HelpSeed PLS
Posted on 04/24/07 12:35:51
Number of posts: 3
I'm looking to run a seed PLS on two separate groups. Thus far I've selected two XYZ(mm) coordinates of interest and have input them into a text file. When I run "multiple voxel extraction" I am prompted to load that text file and then select prefix name and voxel neighborhood size afterwards an error message comes up stating "please remove the following entries....because they are out of the brain." I've tried changing the XYZ(mm) coordinates many times and have triple-checked that the coordinates are within the brain, but the error continues to come up. Is there a way to resolve this or is there another way to get the file to run a seed PLS? Thanks for you help
Sarah
Sarah
Replies:
Untitled Post
I'm Online
Posted on 04/24/07 13:02:24
Number of posts: 291
I tried the dataset here, and I do not have problem if I pick voxels within the brain.
It seems that there are some problem either in the "*datamat.mat" or "*result.mat" files. If you can upload all your session/datamat/result files to you ftp server, and send me the link, I can help you to look into the problems.
My email address is: jimmy@rotman-baycrest.on.ca
It seems that there are some problem either in the "*datamat.mat" or "*result.mat" files. If you can upload all your session/datamat/result files to you ftp server, and send me the link, I can help you to look into the problems.
My email address is: jimmy@rotman-baycrest.on.ca
Untitled Post
I'm Online
Posted on 04/24/07 16:02:29
Number of posts: 291
Hi Sarah:
I received your datasets, and did not find problem when I do voxel extraction.
Here is what I did:
Make sure that in the voxel location file, you put 3 numbers in each line, and each line stands for a voxel. In addition, the number should come from XYZ(mm), instead of XYZ, and this is very important.
Could you please check your procedure and try it again? In case it still doesn't work, please contact me, and I will make sure that you can have your voxel intensities.
Jimmy
I received your datasets, and did not find problem when I do voxel extraction.
Here is what I did:
- I checked your datamat & result file, and they look fine;
- I created a plain text file called "v.txt" in the same directory as the result file sits. In this file, there are 2 lines. The first line is 9 0 9 and the second line is -9 0 9, which means that I want to extract voxel intensity at x=9mm (-9mm), y=0 and z=9mm locations.
- When I click "Multiple Voxel Extraction", I click the voxel location file "v.txt" that I just created, and click open. In the next window, I put tst as the prefix of my saving file name and click save. In the Voxel Neightborhood Size window, I leave it as 0 because I do not want to incude any other voxels, and then click OK.
Make sure that in the voxel location file, you put 3 numbers in each line, and each line stands for a voxel. In addition, the number should come from XYZ(mm), instead of XYZ, and this is very important.
Could you please check your procedure and try it again? In case it still doesn't work, please contact me, and I will make sure that you can have your voxel intensities.
Jimmy
Untitled Post
Posted on 04/24/07 16:23:20
Number of posts: 3
quote:
Hi Sarah:
I received your datasets, and did not find problem when I do voxel extraction.
Here is what I did:
Make sure that in the voxel location file, you put 3 numbers in each line, and each line stands for a voxel. In addition, the number should come from XYZ(mm), instead of XYZ, and this is very important.
Could you please check your procedure and try it again? In case it still doesn't work, please contact me, and I will make sure that you can have your voxel intensities.
Jimmy
Jimmy,Hi Sarah:
I received your datasets, and did not find problem when I do voxel extraction.
Here is what I did:
- I checked your datamat & result file, and they look fine;
- I created a plain text file called "v.txt" in the same directory as the result file sits. In this file, there are 2 lines. The first line is 9 0 9 and the second line is -9 0 9, which means that I want to extract voxel intensity at x=9mm (-9mm), y=0 and z=9mm locations.
- When I click "Multiple Voxel Extraction", I click the voxel location file "v.txt" that I just created, and click open. In the next window, I put tst as the prefix of my saving file name and click save. In the Voxel Neightborhood Size window, I leave it as 0 because I do not want to incude any other voxels, and then click OK.
Make sure that in the voxel location file, you put 3 numbers in each line, and each line stands for a voxel. In addition, the number should come from XYZ(mm), instead of XYZ, and this is very important.
Could you please check your procedure and try it again? In case it still doesn't work, please contact me, and I will make sure that you can have your voxel intensities.
Jimmy
I tried the same procedure with coordinates closer to the origin (i.e. 9 0 -9) and oddly enough it worked. However, when I tried coordinates further from the origin (i.e. 27.0 49.5 2.2 or -25 18 27), I received the "off brain" error message. I've double checked, both in the brain LV plot window as well as in the talairach atlas and those points should still be in the brain. Any ideas?
Sarah
Untitled Post
I'm Online
Posted on 04/24/07 17:20:48
Number of posts: 291
Hi Sarah:
Unfortunately, it was a bug in my code. I have fixed it now. Please download the code from our web site, and try again.
Sorry for the inconvenience,
Jimmy
Unfortunately, it was a bug in my code. I have fixed it now. Please download the code from our web site, and try again.
Sorry for the inconvenience,
Jimmy
Untitled Post
Posted on 04/25/07 14:20:07
Number of posts: 3
Hey Jimmy,
Looks good now. Thanks for all your help.
Sarah
Looks good now. Thanks for all your help.
Sarah
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